pokeshifters-shadows rising
by conmanay
Summary: cipher has returned and is rebuilding their shadow pokemon army. now a new group of heroes must rise to stop them. Will they succeed or will darkness rule all (first story)(accepting OCs) (better after the first chapter)
1. Chapter 1

Chapter 1

It was a dark cold night in viridian forest. Everything seemed normal, as if the forest itself was at peace. However if one looked closely they would see a group that certainly didn't belong there. Hidden by the veil of their illusion a pack of zororark were finally at peace after a day on the run. A mother was putting her cub to rest. He was sound asleep, blissfully unaware of the world around him. The mother zoroark seemed happy looking upon her sleeping son. "What a little angel" she thought as she laid down to rest herself. As she laid there she thought about the time spent with her son. Despite him being only 5 years of age he was maturing fast. He could speak cast illusions with ease and even wanted to hunt soon. However her happy thoughts were soon replaced by that of her fearful ones, her son, while seeming normal in every way he was in fact far from it. She knew deep down a day would come soon where she would have to reveal the truth. She still hoped that day would never come. As the pack rested a group of heavily armed men closed in, their night vision goggles cutting through the darkness. The pack were blissfully unaware of the horrible fate about to befall them. once in sight the commander gave the order in a hushed voice "weapons free take the cubs alive kill the rest" within seconds hot lead cut through the pack the zoroarks were helpless . Within seconds it was over. Only one cub survived the rest of the pack laid dead the cub was loaded in a cage and taken away. The commander was furious with his men "you idiots we needed them for research" he yelled. "the master will not be pleased" he though as began the walk back to his chopper. As he walked he had a devious smile on his face "soon cipher will rule this world


	2. Chapter 2

Chapter 2

Jake's POV

I hate math…..

That was all I could think of as I sat in class my mind slowly dying, why was this useful I would never use this outside of school. After an eternity the bell rang and I was free at last I walked out the school doors I wondered how I would survive finals. I walked home in silence ignoring all the people and Pokémon around me I pondered something that high school had made very sure of to remind me of. What was I going to do when I graduated? This was a hard question to answer. Always has been especially because of my condition…. You see I am what is called a shifter, at least that's one of the names for it. it's what I prefer at least. Shifters have the ability to turn into a Pokémon at will in my case an umbreon. How you ask, well it's complicated. It's a rare genetic trait that some people have about a 1 in 2000 chance. It's impossible to detect the gene without very sophisticated blood work. That's all I know really also some of you may be asking do you have to crawl out of your clothes. Answer yes and no, tight fitting clothes you can take with you then when you change back they are still there. Only my parents know about it I honestly prefer it that way I'm shy enough and being called a freak would NOT help. I was almost home when I got a chill down my spine I felt like someone was watching me. But unsurprisingly no one was looking at me I shrugged it off and went home…

? POV

I walked up to the doctor as he quickly closed his laptop "what are you doing doc" I said sternly "just cleaning out my email" he said as calmly as he could "whatever….. what's the status of the factory, the master wants a report" I said. He started sweating. I knew he was behind schedule and he was trying to cover it up what a coward. I sighed "you know how the master feels about failure" I said "rest assured the factory will be producing shadow Pokémon 20 per hour within 2 months" he said with fear in his eyes. "I hope so for your sake doctor" I paused "what about subject XJ236 I hope your making better progress with that zorua considering the trouble we went through to get it" "that zorua is more than meets the eye believe me" he said confidently "I hope so doctor , I hope so".


	3. Chapter 3

Chapter 3

Michael's POV

This is bad. I though as I was sitting at my desk, attacks via trained Pokémon was increasing primarily in Jhoto and Hoenn. Even more suspiciously those trainers were never found and prosecuted. It wasn't a major spike, but still concerning. However that would not be enough to warrant an investigation by the MRPA. The MRPA or multi-regional-protection-agency was an organization of action but not before it had sufficient cause to intervene. I started working for them when I as 21 and after 5 years it was still as interesting as ever. I trusted them, sure but I always think they are too slow to action. That was not my main concern however. Cipher… that name still gave me chills. Even after their defeat 11 years ago I always was paranoid about their return. Many people though that cipher was only operating in Orre but that was never entirely true. There were small black sites all over the world but all of them were supposedly destroyed soon after Greevil's defeat. I may be too paranoid about it but most shadow Pokémon appear normal outside of combat. They are impossible to identify without the proper equipment. I just sighed as I closed my laptop, woke up my sleeping Jolteon and went home for the night.

Lilly's POV

I sat at home doing my homework. It was a normal night, say hi to mom, eat dinner and go to my room. I was sitting there when a though crossed my mind, one that had not surfaced in years. I wonder how my father's doing. He left my mom when I was 8 not because of her but because of me. I'm a shifter I can become a kirlia at will. I can read minds even when I'm human. My mom didn't care about it but my father just snapped. He said that he would not have a freak for a daughter and left. I've managed to get over it but it hit my mom hard. She still thinks about him a lot. I shook the thoughts from my head and continued my homework I was just about to close my textbook when I got a nasty feeling in my stomach. I just had an itching felling something bad was about to happen. I went down to check on my mom. What waited for me was far worse than I expected my mother was on the ground out cold, but was still breathing. 6 men with body armor and guns were in my house all looking at me I was just about to shift when a searing pain hit me in the back I fell on the floor I fought to stay awake but another zap in the back and I lost consciousness.

? POV

"That was easy" I said as the girl was laying on the floor out cold. "Man the doc did a good job on these stun batons" I said to my squad. "Anyway put a shift collar on her and take her to the chopper" I ordered. My squad picked her up, attached the collar and carried her away. Just then the mom began to wake up. I just sighed, "Sorry lady but you've seen too much I activated the blades on my gauntlets and finished her off quickly. I may be an assassin but I don't like unnecessary suffering. I walked to the chopper and we took off. "Call base" I said, tell the doc we have his new test subject


	4. Chapter 4

Chapter 4

Lilly's POV

I woke up in a large room it almost looked like a colosseum, like where the last championships were televised from just slightly smaller. I was just standing up when a sharp voice called out from nowhere. "Ah I see you are awake, very good time to begin the experiment". "Who are you, take me home now" I yelled at the voice. "My dear girl this is your home now"." W-what" I said in a fearful voice." I am Doctor Joseph Gregavich and you are the beginning of our great undertaking" the voice said. I'll never help maniacs like you" I said fiercely. Just then a searing pain went through me like my entire body was on fire, "disobey and there will be pain", the man said. After the pain subsided I noticed a large collar around my neck it was made of black metal and had strange lights and circuits on it. "What is this thing you put on me" I said. The voice laughed briefly then spoke "that is a shift collar it prevents you from shifting or using you powers but it can still shock you, however I deactivated that feature once you were in here. After all you can't even see where we are let alone harm us" he said proudly. "What do you want from me" I asked angrily. "My dear girl you are to be a test subject for a new serum I've developed". "Now shift into you Kirlia form" he said. "Go to hell" I responded. In seconds another painful jolt shot through my bod, I fell to my knees in agony." Cooperate or I'll keep going" he said as the pain began to subside. I gave in and shifted, after a brief flash I was in my Pokémon form. The room seemed even more massive that before since I'm smaller as a Kirlia. "Now then let's see what you are capable of" he said in a sinister voice. Suddenly a small door opened and an Ariados came out its beady eyes looking straight at me. The large spider Pokémon spat a sludge bomb at me; I reacted just in time and jumped out of the way, barley dodging the filthy sludge. Then it rushed in for a bite attack its two fangs glowing white I knew I couldn't out run it so I decided to make my move. Just as it was about to bite me I side stepped and shot a will-o-wisp at it. The purple flames hit the Ariados hard. It still was up and fighting but I could see it was weak, it began to crawl towards me but I quickly used psybeam on it. The multicolored beam hit the Ariados sending it flying it hit the ground hard; it then tried to stand back up. However it was too weak and fell back down unconscious. I was breathing heavily but managed to shift back into a human. Man was I lucky that I trained myself to fight otherwise I would have been screwed. Just as I changed back I heard the doctor's voice again. "Well done, you are very skilled despite being only 16, you have passed the first test, and after a few months of daily tests it will be time for the serum" he said. "Men sedate her and take her to her cell" as he finished saying this two men with stun batons came in I tried to shift but nothing happened. I felt a needle go in my arm and I lost consciousness soon after.

Gregavich's POV

I smiled as the girl was taken out of the arena. "A perfect first trial "I said. "Well done doc a perfect candidate" a voice said from behind me. "Ugh why do you have to be here again, I don't need an assassin as a body guard" I said. "Because the master needs an overseer for you and this facility's security" he said bluntly. "I send him a report on you progress, what materials do you need again doc" he said. "I need those DNAs samples you promised me and more shifters" I said. "Consider it done doc" he said casually as walked out of the observation area.


	5. Chapter 5

Chapter 5

Gregavich's POV

I watched closely as the zoroark was moved to its new cell. Finally after a month of testing I figured out its biggest use to us. The shadow energy we use to make shadow Pokémon is a processed from of an element we call dark matter. Every dark type Pokémon has some in its body, but not enough for our needs. This zoroark after it evolved started showing a massive reserve of dark matter. If my hunch was correct we could power the entire factory indefinitely as long as it is was alive. After it was shackled I started my device. The room itself has special energy extractors in the walls, making energy harvesting easier and safer. However the extra energy is not the most curious thing about it. After a few DNA tests I found something astonishing, it does not age at all. How you ask, well its cells seem to constantly regenerate so rapidly that it doesn't physically age. Not to mention it's immune to poisons and its rapid healing. It got its arm sliced open and it healed in seconds. However containing it no easy task, all the handlers that try to subdue it are either scratched up severely or lost a limb. Even though it developed immunity to our tranquilizers I managed to find an alternative method to subdue it, pain. Enough pain subdues anything. As my thoughts drifted I looked up at the collection tank. It was full already! I quickly started the converter and collected the fresh shadow energy. "Start the production line" I said over the intercom. Soon the conveyer belt flared to life and the pokeballs went into my masterpiece, the corruption engine. Mere seconds later the pokeballs emerged. I checked the monitor above my control panel. All power levels holding steady. The monitor then displayed the message I've been waiting months to see. "Corruption complete" the computer said. "Success at last" I said as the production line continued its work. Just then I heard a cold voice behind me. "Well done doctor you have excided expectations". I turned and faced the monitor behind me. "Thank you master….. Are my samples on the way" I asked respectfully. "Yes doctor they are, now that the factory is operational focus on phase 2" he said calmly. "as you wish sir" I said. The monitor turned off **and** I walked to my lab. "Soon our army will be complete"…..

Jake's POV

I sat at the table eating with my sister. My parents were out for dinner. My sister is also a shifter she can become a glaceon. She is 14 while I'm 17. Unlike most siblings we got along well but I always felt she was smarter than me but me and her looked out for each other no matter what, unlike me she's a social butterfly, I don't know how she makes friends so easily . As we ate I heard a small noise outside but shrugged it off as the wind.

? POV

"Two shifters are inside no one else" I said quietly "switch to tranquilizers" I ordered. My squad readied up. "Two more shifters all alone, alright boys lets tag and bag"

 **Authors note- I would like 2 OCs it would help me greatly**

 **If you want to submit one please tell me what their name, age, personality and shift form is in a PM**


	6. Chapter 6

Chapter 6

Kelly's POV

As I was eating I heard shuffling outside. "Jake someone's outside" I said nervously to my brother. I always had good hearing, probably due to being a shifter. "Probably just mom and dad" he said casually just then a bang hit our sensitive ears. Seconds later a small metallic ball rolled in from the hall way at our feet. I never could have reacted in time. There was a flash and everything went white and my ears were ringing. With my senses going haywire I could not see or hear anything. Then a massive force hit the back of my head, soon after I felt hands around me I was lifted to my feet just as my eyes came back online. 4 men with guns and body armor were holding me and my brother by our arms they were muttering something I could not understand for a second, eventually my ears stopped ringing and I heard them saying "let's make this quick". Then I heard a distorted voice that sounded like a mix of human and computer say "get those collars on now!" I then felt a weight around my neck as I looked over at my brother , a man in black armor gave another order, "let's move double time" the men put a large black collar on my brother. "What are you doing" I said as sternly as I could. We were dragged out of our house as a black helicopter touched down nearby. The prop wash blowing my hair around. Just as the men were about to shove me in the chopper I heard a voice yelling an order " jolteon thunderbolt!" Out of nowhere a bolt of lightning hit the ground, zapping the 4 soldiers but the man in black armor merely flinched . As the men fell to the ground twitching the black armored man flicked his wrist causing axe-like blades to appear on his arms. Then a man with a jolteon at his side came out of the dark night, he had medium length ginger hair and green eyes that showed of a fierce resolve. He had a strange earpiece on that seemed out of place on him. "Let them go" he said in a stern voice. The black armored man said nothing but charged at him with incredible speed. Just as the armored man's blades were about to slash his opponent the red head sidestepped and pulled out a gun with a yellow barrel. Two needles shot out of the gun sticking into the assailant's armor, there was a small burning sound and the man fell to his knees. Then 6 swat soldiers appeared with assault rifles all aimed at the black armored man. "Your surrounded come quietly" the officers said. Then the assassin pulled out a pokeball and tossed it in the blink of an eye. A pigeot appeared from the orb and flapped its wing blowing strong wind everywhere. The swat team was distracted just long enough for the black armored man to jump on to the large bird Pokémon and take off into the night. As me and my brother stood up, the ginger haired man's earpiece activated putting a glass lens over his eye. He looked shocked as he produced a phone from his pocket. "Command this is Michael I just encountered a man with a shadow Pokémon" he said in a dead serious voice. A few minutes later he hung up the phone and walked up to us as we got those collars off. "You two must have a lot of questions" he said as the 4 soldiers were loaded in a swat van. You need to come with me to HQ" he said calmly. I looked at Jake; he nodded to me as we were ushered into a car and drove away from our home.


	7. Chapter 7

Chapter 7

? POV

I grinded my teeth as I walked into the compound. What are the odds that he worked for MRPA, just my luck? Not only did I fail to secure the targets but I had to use a shadow Pokémon to escape. The master will surly punish me for my failures. I walked into the lab as the doc was over a microscope. I quietly passed by him hoping he wouldn't notice me. "Where are you going" he said in a snide voice. I stopped dead in my tracks. "Judging by your demeanor you failed to secure the assets didn't you". "Yes" I said through clenched teeth. He simply chuckled and sent an email on his laptop. Within a minute a video monitor came on and a cold voice echoed through the room. "How disappointing Alex" the master said in a mocking tone. I fell to my knees in front of the screen "please forgive me master" I begged. "Fear not you have proved you use many times, but fail me again and you will be punished severely" he said in an emotionless tone. With that remark the monitor turned off and I sulked off to my quarters to sleep.

Gregavich's POV

I was still chuckling from Alex's predicament as he left the room. Serves him right for being such a smart alec to me and everyone else, he got what was coming if you ask me. As I refocused on my work the DNA sample dissolved into the serum. "Perfect, now it's time for the test" I walked to the observation room and gave an order on the intercom. "Bring the girl to the arena its time" I said. Soon we would see if phase 2 was ready. Either it works or the girl's body may react violently and kill her, either way ill have some interesting data for sure.

Jake's POV

We were driven in a car with blacked out windows. After 2 hours we arrived in a large garage with all sorts of strange vehicles and jets. We were ushered into a room that looked like an interrogation room and told to sit down and wait. 5 minutes later the ginger haired man walked in with a calm smile on his face as he sat down across from us. "Pretty scary dudes huh" he said casually. Me and Kelly said nothing. "Anyway my names Michael" he said kindly. "Thanks for helping us" Kelly said in a shy voice. "no problem it's what I do" he said casually. "Where are our parents" I asked. "They're at you house I filled them in" he said. "Unfortunately you can go home yet" he said in a sad voice. "Why" we asked in unison. "Um you two are shifters and you almost got kidnapped because of it by a man with a shadow Pokémon" he said bluntly. "Rest assured you'll go home eventually but for now you'll have to stay in protective custody "he said obviously trying to calm us down. "Come with me ill find you a place to rest" he said. We looked at each other and followed him out of the interrogation room.


	8. Chapter 8

Chapter 8

? POV

I sat there in silence thinking of only one thing, escape. I knew these people we stealing energy from me I could feel it. The longer I was stuck here the more dangerous they become. After 2 months of planning I finally am almost ready to enact my plan. There's just one problem, how do I get out of these shackles? After that I was fine but these shackles were the biggest obstacle, just then a though struck me. Yes that could work, it was risky but it just might work…..

Lilly's POV

I was taken out of my cell right after I woke up. I knew this was it; it was time for the serum. The doctor was defiantly ready after a month of tests. I was soon in the arena there was a large metal chair in the middle of the room I was forced in it and strapped down. The door opened and a man walked in, he had black hair that was cut cleanly. His eyes were trained on me, and a vile smile was on his face. As he walked up to me he produced a syringe from his black lab coat. Then he spoke in a maniacal voice that I knew all too well. "It's time my dear girl, you are the beginning of my greatest achievement" he said proudly. "You'll pay for all you've done you monster" I said with as much force as I could. I would not give him the satisfaction of begging for mercy. All of a sudden alarms went off and the doctor put the syringe back in his pocket. He motioned for two guards to come over and gave an order. "Keep her here, don't give her an inch". He said as he turned around and left the arena.

? POV

My body was aching but at least I was free of the chains, I overloaded the energy extractor and it blew off my shackles. Now I had to wait, the second the guards came in I would have to sneak out the door using my illusions. I quickly made an illusion of me still in my shackles. Hopefully it would buy me enough time to get out. The door opened and I walked right past the guards while they were focused on the illusion I grabbed one of their keycards and shut the door. I the used an illusion to disguise myself as a guard and ran though the hallways I found a door and swiped the keycard, it didn't work at first but I swiped it again fearful that I would have come so close yet failed. The door opened and I walked away casually as a guard. As soon as I was out of sight I dropped my illusion and ran. As I ran I felt relived as I breathed fresh air for the first time in months. I had escaped. At last I was free

Gregavich's POV

I banged my fist on my lab table as I was given the report. It escaped, it escaped I just couldn't believe it. I fear the master will not be very forgiving of me. This is a major setback, without that zoroark we don't have anything to power the factory. As I sat there thinking of options the door behind me opened. I didn't bother to turn around. "Doc you have a.." I interrupted him soon after, "I don't have time to deal with you Alex. "I hoped for a better welcome doctor" I knew that voice. I turned around and looked at my visitor. I was in shock the second I saw him. There he was, the master was right in front of me, four Bisharps around him with all their metallic eyes glaring at me. I fell to my knees "forgive me master, I know I messed up but I do have some good news" I said fearfully. "And what is that" he said coldly I stood up my legs shaking. "The serum is ready I could test it right now" I said. The master paused for a moment his eyes drilling into me. Then he spoke as calm and emotionless as ever, "very well doctor I will watch the test personally then decide you punishment" he said in a ruthless voice. I stuttered at that remark "b-but it may not work and…." "Silence!" the master said in the loudest voice I've ever heard him speak in. "if you are confidant in your work then there is no need to worry is there, now show me to the observation room" he ordered. I nodded and took him through the halls. This was it, either the serum works or there's no tomorrow for me…


	9. Chapter 9

Chapter 9

Lilly's POV

I sat in that chair for at least an hour, it was worse than anything they've done to me. Just sitting there waiting for the inevitable. After what seemed like an eternity I heard a door open. Then the doctor walked in with a syringe full of a red liquid. He was smiling as he quickly washed the syringe and put it in what looked like a robotic arm. "Anything you'd like to say girl" he said in a mocking tone. In response I spat in his face. He simply wiped his glasses off and left the room. 5 minutes later the arm activated and I felt the needle go in my arm. Within seconds my body began to burn. The pain was far worse than the shock collar had ever been. I fought to stay awake but the pain was too great and I passed out fearing I would never wake up.

Alex's POV

I sat there in the observation room waiting for something to happen. The girl was unconscious but she was flailing around in the chair. After a few seconds her body went limp. "Well done doc" I said sarcastically. Just then a blinding flash appeared in the room. Seconds later the light faded and looked into the arena. What I saw was unbelievable, a Latias was laying there breathing hard but alive. I was awestruck I could find any words to speak. The doc had done the impossible he had created a legendary Pokémon out of a single feather. He reacted quickly and sent two handlers to move it to a new cell. The master had a smile on his face as he walked up to the doctor. "Well done doctor you pulled it off, now can I expect more legendary Pokémon on the way?" he asked in a sharp voice. The doctor smiled and spoke with newfound confidence "yes you can if I have the shifters and DNA I need" he said. The master spoke in a calm but slightly joyful tone. "Very well doctor, consider it done" he then turned to me and spoke in a harsh voice "Alex while the doctor continues phase 2 I have a task for you, find that zoroark by any means. I stood I front of him and said "yes master you can count on me". "I hope so Alex" he said as he began to walk out of the room. Before he left he said one more thing to the doctor "don't forget your place doctor" he said. "Yes master Ardos" the doctor said as he went back to his lab.

Michael's POV

I sat in the command center with my jolteon at my feet. What's next, cipher's back and we have no idea where they are or what their next move is. "Hey Michael why the long face, well figure this out" a voice said from behind me. "Cassandra, back from your op already" I said casually. "Yea and I have orders from the director" she said in a serious tone. "Those two shifters you saved, he thinks we should recruit them" she said in a serious voice. "No not a chance they are not fit to be agents" I said almost yelling. "I know there young but they may be just what we need to give us an edge" she said. She was right, but they would need to agree to it and she would have to train them. After a few more minutes of mulling it over I realized I wouldn't win an argument with her. "Fine I'll talk to them" I said. I sighed as walked towards their temporary room; this was going to be a long night.

 **Author's note- thanks to emikat1234 for his OC of Cassandra, now I just need some bad guy OCs**

 **Anyways leave a comment like or review it keeps me writing after all.**


	10. Chapter 10

Chapter 10

Jake's POV

This is better than school at least, I though as I continued my hand to hand combat practice. It had been 3 months since me and Kelly joined the MRPA. Needless to say there was never a dull moment. Training was tough, Michael made sure of that. However I liked our new instructor more, Cassandra was a shifter a Hydregion to be precise. I guess that explains why she has purple highlights in her brown hair. She was nice, but you could not win an argument with her. If she had an opinion on something she would make it known. We had a few missions but they were mostly just checking out old warehouses and forests in hopes of finding out Cipher's whereabouts. As I continued hitting the practice dummy I thought about my other training. The snag machine was definitely vital; after all it was the best way to subdue shadow Pokémon. Me and Kelly were doing well but I always felt that all this training was for nothing. Just as I got ready to start on the dummy again Cassandra's voice interrupted me. "Ready up I've got an actual mission for you" she said. "Really I've heard that before" I responded. I sighed "what's the briefing?" "Four people badly injured all found outside Eterna forest" She said. "I perked up at that, "alright let's get to it" I said as I picked up my snag machine and headed to the hanger.

Alex's POV

I sat in the factory's command center rubbing my forehead. Where was he? I've been searching for him for months, but nothing except dead leads and cold trails. As I was deep in my thoughts a voice spoke in a mocking tone "still having trouble Alex" the doctor said in a condescending tone. "Don't you have something better to do than mocking me" I said angrily. "No not really I've got the serums prepped but without shifters I can't use them and you still haven't retrieved my battery for this factory". I was about to yell at the doctor when one of my soldiers came in. "sir we have a hit, the scrambler intercepted some chatter about Eterna forest from the MRPA". I stood up and put on my gauntlets. "Alright let's move out get 3 squads ready and prep the chopper". "Yes sir" with that he left the room. I walked out of the command center heading towards the hanger with one thing on my mind, "I'm coming for you Connor"

Connor's POV

I sat in the forest eating some oran berries, The sweet juice rolling down my throat. That lab's food was the worst. My mom always found good food, my mom…. gosh the thoughts of her were worse than anything else I've endured. I miss her so much, but she's gone nothing can change that. My heritage was always a mystery to me up until a month ago. At least I finally know who my dad is. That's why I was in Sinnoh, training myself using what he taught me. I would need it for what was ahead

 **Flashback**

I quietly walked around the forest on New Moon Island. I didn't know why but I felt like I should come here, that I had to be here. I was walking when I heard a voice. This voice however was different, like it was in my heard somehow. "Took you long enough to get here" a dark and raspy voice said. I heard a sound behind me and I turned around quickly ready for a fight. However In front of me there was a figure floating above the ground one that certainly scared me. It had long black arms with three sharp fingers; and it had large blue eyes that were slightly obscured by its white mane that looked like smoke almost. It looked like a ghost from a horror story. "Who are you" I demanded. "The creature chuckled then spoke "I am Darkrai and while you may not believe it, I am you father.

 **Flashback end**

Soon after that we started training, and man was it tough. It took a while to even use some of my abilities without passing out. He taught me how to use powers that only I had, dark void, nightmare, teleporting and so on. Finally after a month of daily training it was time for me to leave; he said that he had to be left alone, that it was dangerous to get attached to him. Even though I objected he just disappeared. So I left the island and began to wander Sinnoh, moving locations every week. I have to keep moving to avoid being found by Cipher. As I finished eating I heard a rumble overhead. Someone's here. I can't run, they probably have the perimeter of the forest surrounded. I'll have to stand and fight.


	11. Chapter 11

Chapter 11

Jake's POV

As the helicopter touched down I was edge it was almost night, Kelly was too. Cassandra and 5 swat soldiers were following us. As I walked with Kelly I thought about what could be waiting for us. Best case- just a blood lusted Pokémon, worst case- a cipher base. If that were the case I had my snag machine ready. I was snapped from my thoughts by my sensitive ears; something was circling us, something as big as a human. I held up my hand "hold, look around there's something watching us. As I said this a red blur emerged from the forest in a split second. I was knocked down and I heard gunfire. I quickly shifted into my Umberon form. As I stood up I saw my attacker. A Zoroark was moving almost too fast to see it; the entire swat team was out cold. Strangely they were shaking on the ground muttering, like they were having a bad nightmare. Cassandra and Kelly were also shifted. Cassandra shot a dragon pulse but the zoroark sidestepped the energy blast while using an attack I've never seen before. The black orb almost looked like shadow ball but seemed different. It must be a shadow Pokémon! I quickly use moonlight to heal myself. Once I was recharged I launched a dark pulse at the zoroark. It turned and simply raised its hand as the dark pulse hit its hand and it disappeared. I was in shock, how did it absorb that attack so easily. Just then an ice beam hit the zoroark in the back. Cassandra reacted quickly shooting a hyper beam. The powerful blast hit the zoroark and it staggered but seemed fine. The zoroark was just about to launch another orb when 5 darts shot into it torso, it fell to its knees but stayed awake everyone shifted back to human at once ready in case these were hunters. Then I heard a voice I knew and feared, "stand down and come quietly, your surrounded". Suddenly a black portal appeared at the zoroark's feet, it jumped into the hole and vanished. "Darn we were so close, well at least we have three shifters for the doc" the black armored man said. He activated his blades and lunged at us I dodged, just as I heard Cassandra shift. I knew what she was thinking; I shifted into an umbreon and jumped on her back, Kelly was just about to shift as well when 4 darts hit her in the arm, she fell to the ground. Cassanrda flew off with me on her back as I was yelling "we have to go back for her!" I yelled. "There's too many, don't worry we'll find the base she'll be at soon" she said confidently. "How" I asked. "There's a tracker in her snag machine. I sighed as we flew back to HQ. "Let's just hope we are not too late" I said grimly

Alex's POV

I strapped the girl in the chair just as she woke up. "Let me go" she demanded. "I'm afraid that is not possible my dear girl" the doc said as he put the serum in the injector. "w-what is that stuff" she said nervously. "The future my dear, the future" the doctor said as me and him walked out the arena.

As the girl struggled in her chair I looked at the doctor. "Why no tests doc?" "because the serum is perfected and she is already in shape" he said in an irritated voice. The doc pressed a button and the needle went in the girl's arm the doctor smiled and turned to one of the guards. "Get a cell ready, this subject will be hard to contain" he said as a bright flash filled the arena


	12. Chapter 12

Chapter 12

Kelly's POV

I woke up in a large room that looked like a containment cell I noticed a weight on my head. I tried to stand up on two legs but I couldn't. As my mind came back online I looked at my legs in horror. I had aqua blue fur with white patches on it, my hair was longer that I thought it could be and I had a large white snout. I wasn't a Glaceon, I was something else entirely. As I shakily stood up light flooded the room and a voice emanated from the walls. "It's awake, how fortuitous I was just about to make it wake up". That voice, that vile voice filled me with rage. I looked around me but I couldn't see the doctor. "Ah so you are ready to fight" he said in a jolly tone. Suddenly two men with guns came in, I reacted and shot a blizzard at them. The two thugs were frozen solid, as I stood there looking proud a burning pain went through my body, I fought to stay awake. Suddenly I felt water in my throat I concentrated on that feeling, I opened my mouth. A huge blast of compressed water shot out of my mouth making a dent in the cell wall. Just then pain intensified, as fell to the ground losing consciousness as I heard the doctor's voice. "Be a good Suicune and stop resisting" he yelled. Despite my will I passed out soon after due to the onslaught of pain.

Gregavich's POV

As the Suicune was moved to the arena I looked at my lab assistant. "How did it make a dent in that cell!" I demanded. "It's supposed to be impossible to even scratch". My assistant was sweating, too scared to say anything. "never mind I'll just have to check the shields later, get that Latias sedated and move it to the arena it's time for a sparring match". I ordered. "Yes sir" he responded as he turned and left the room. "Time to see what these two are made of" I said as I walked to the arena.

Michael's POV

This is not going to be easy, I thought as we looked over the recon of the factory. It was heavily guarded to say the least. Anti-air batteries everywhere and reinforced steel doors at every entrance, and that was just the outside. As we looked over our options Jake stood up and spoke confidently "I have an idea. "And what is that" director Malcom said. Jake pointed to the corner of the factory, "there's a submarine bay here right". Everyone in the command center looked at Jake curiously. "We could have a frontal assault at the main gates to buy time for a scuba team to get inside". The director looked impressed. I spoke up first "I can lead the frontal assault while Jake and Cass lead the scuba team" I said. The director paused then nodded." Alright then, Michael get your men ready". I nodded as the director looked at Jake and Cassandra "you two get suited up for a swim". The director then stood up and looked at the entire room. "Alright primary objectives- shut down the factory and rescue any test subjects, and if possible capture the scientists and any data you can find" he said in a serious tone. "I want everyone wheels up in 4 hours" he ordered. I walked out of the command center with only one goal in mind, stop cipher at all costs.


	13. Chapter 13

Chapter 13

Gregavich's POV

I zapped the two legendary Pokémon awake once we were ready; Alex was right next to me. They've slept enough for one day, as they got up they seemed to be talking to one another. I quickly zapped them and said "no talk, fight or I'll up the voltage". They began soon after that, and I must say it was a sight to behold. The suicune was doing well at attacking and predicting the latias's moves shooting blasts of ice and water with incredible force. While the latias was too fat to hit its psychic attacks were impressive as well, they went back and forth for about 5 minutes then stopped briefly to rest. Just as I was about to encourage them again alarms went off piercing my eardrums. A guard came in franticly yelling "sir it's the MRPA they've found us". I looked at him with disbelief, "how could this be….. never mind send out all available soldiers and shadow Pokémon, we'll crush them before they even get inside". As he ran off to relay my orders I looked at the arena. After a moment of thought I made a decision. "I'll sedate them but keep them in the arena, Alex you're in charge of keeping them contained don't let your guard down for a second". As he nodded I activated my micro injectors in their collars. They fell to the ground unconscious as I walked to the control room. The MRPA has no idea who their messing with…..

Michael's POV

The soldiers all had their guns pointed at the gates as it opened. Cipher soldiers poured out of the door as we opened fire. The gunfight was in our favor until their reinforcements arrived. At least 40 shadow Pokémon arrived and began to pummel our men. Most were too tough for bullets to even scratch; I readied my snag machine and began to throw snag balls as the chaos continued around me. I just hoped Jake and Cass were having better luck.

Jake's POV

As I held on to the sub pod I was nervous, the cold, black water was definitely not helping. As we arrived at the submarine bay I noticed one sub was docked. I looked at the scuba team and motioned to the sub "plant charges on the bow and stern but don't set them off, we can't reveal our position yet". They nodded and began to work. Once that was done we found our entry point. A large metal grate that led to a sewer pipe, I pulled out my C4. I planted the sticky explosive and motioned for everyone to get clear. There was a muffled bang and a hole was blown in the grate. "Alright let's move" I said as we entered the pipe. As we swam up the pipe I thought about Kelly. I'm coming for you sis, just hang in there, I thought as we neared the end of the pipe.


	14. Chapter 14

Chapter 14

Michael's POV

As the last shadow Pokémon were snagged the remaining cipher soldiers fled inside the factory. They knew they had lost for now. I motioned for my men to peruse and we followed them across the factory yard. The large doors closed just as we arrived. The reinforced steel was defiantly a problem "Humph, well get some fire types and lets start cutting".

Jake's POV

As we got our wetsuits off I heard an intercom announcement. "All available soldiers fall back and protect the entry points". I motioned for my squad to follow and said "alright let's get as far as we can without attracting attention". As we walked down the hallways I was ready for anything, the adrenaline pumping through my body was making me jumpy. We found a room with a sign that said data vault. I motioned for the squad to stack up and I shifted. Once I was ready Cassandra cracked the door and threw a flashbang. I walked in slowly, looking everywhere. Just as I was about to shift back a soldier holding a gun appeared from behind a chair. He was just about to fire but I launched a dark pulse knocking him on his back. I shifted back and pulled out a flash drive as my squad watched the exit. I uploaded everything I could but most of it was protected, we would need a retinal scan form a high level officer to get at those files. As the download finished I brought up the map of the factory and looked for where my sister could be. As I looked at the map I heard footsteps coming down the hall. "Hurry up Jake" Cassandra urged. "Working on it, let's see labs, production, arena, I got it holding cells this way" I pointed as we locked the door and ran down another hall.

Gregavich's POV

I looked at the outer cameras nervously. The MRPA was cutting though at multiple entry points. I looked over at the arena cameras and noticed the two test subjects were being moved to their holding cells. "Alex!" I yelled over the intercom. He looked at the cameras clearly agitated. "What, doc we have to move them before they wake up" he said quickly. I was about to argue when a massive bang hit my ears. The MRPA was inside the factory. I looked at the cameras and then spoke to Alex again. "Fine, but if you aren't watching them take your men and protect the corruption engine" I ordered. Alex nodded and walked out of the cameras view. This was not looking good…..

Connor's POV

I looked at the factory from a distance. This was perfect, while they were busy fighting each other I could do what I came here to do. I opened a portal and warped inside. That traitor is going to pay, I though as I ran through the bright hallways.


	15. Chapter 15

Chapter 15

Jake's POV

As we arrived at the holding cells I noticed that the soldiers were just leaving the area. I motioned for my squad to wait until they left. As soon as they were out of sight I looked at Cassandra and whispered. "You take the cell on the left, I'll take right" She nodded as I looked at my squad. "Watch our backs; tell us if anyone's coming". As they fanned out I looked at the door. This is it I just hope she's in there. I took a deep breath and opened the door; I could barely believe my eyes. A Suicune was sitting there. A legendary Pokémon was a few feet from me. I shifted into an Umbreon and walked up to it slowly. As I was looking at it started to move I jumped back in fear, I just hoped it was friendly. Then it spoke, "Jake is that you". I recognized that voice instantly, "Kelly?" I asked the Suicune in a worried tone. As it stood up it smiled and spoke "yea it's me" she said. I was awestruck, but I mustered the will to talk. I had tears in my eyes as I looked at her "are you stuck like that?" I asked fearing the answer. "Maybe" she said grimly. I was on the verge of crying when she said "but if you get this collar off we can check" she said with hope. I quickly shifted and used shadow claw to break the collar. She closed her eyes and concentrated, at first I was scared that she was stuck, but soon there was a bright flash and my sister was before me. I hugged her as soon as the light subsided. "I thought I lost you" I sobbed at I hugged her. "Me too" she said tearing up. Once I got myself together I noticed her hair was dark purple just like a suicune's mane. We left the cell just as Cassandra walked up with another girl. She was tall and had black hair. She was smiling but she seemed very nervous. I immediately noticed her eyes were a very strange orangeish yellow. She was standing there behind Cassandra almost trying not to be noticed. "This is Lilly" Cassandra said breaking the silence. "Hi" she said in a quiet voice. As we stood there we heard a loud bang. "Let's get out of here" I said remembering our current situation. "Wait" Kelly said. I looked at her confused as I began to walk away "what is it we have to get out of here" I said. She grabbed me by the arm and looked me straight in the eye "we have to get the head scientist before he gets away" she said firmly I looked at Cassandra and back at Kelly as they both nodded. I knew this argument was only going to go one way. I looked at my squad "get Lilly out of here" I ordered. They nodded and headed down a hallway with Lilly in tow. I looked at Kelly and said "let's move before he escapes" they nodded as we ran towards the labs.

Gregavich's POV

"This can't be happening" I said as I looked at the cameras. Both test subjects were free and the MRPA was pouring through the lower levels. I banged my fist on my table cracking the glass words could not describe my anger. I quickly regained my composure and came to a decision; it was the only option left. I looked at my lab aid and said "get my notes and ready the chopper for takeoff" he nodded and ran out of the command center. I walked up to a monitor and held up my eye. "Identify confirmed, welcome doctor" the artificial voice said. "I paused for a moment and shook my head. It's too late to do anything else. I then spoke my command "initiate reactor meltdown, disengage all cooling pipes and delete all server data. "Very well reactor meltdown initiated; core detonation in t-minus 35 minutes. I quickly ran toward my lab. The serums must be saved, I thought as the clock ticked in my mind.

Alex's POV

I heard alarms going off as i ran through the hallways leading to the lab; I didn't care what they meant. I had to help the doctor. Out of nowhere a unseen force hit my side. I felt nothing but pain as I was flung though a wall into the arena. As I stood up I saw him, what a fool he was coming after me. "you should have ran and hid" I taunted him. He looked at me his eyes full of hatred as he said "you sold out the pack, you killed my mother" he yelled. "Yes, yes I did" i said casually. I smiled and said "you know very well that I simply had to insure my own survival" I said. He barred his fangs and said "I am going to kill you, right here right now". I activated my blades and dropped my illusion as I spoke. "Oh yea bring it on" I


	16. Chapter 16

Chapter 16

Connor's POV

I stared at him with hate, watching his every move ready for him to attack. "Time for you to meet your end you traitor" I said breaking the silence. He said nothing in response, "what scared to face me" I taunted. He still just looked at me. "What did that doctor make you his personal… "You are the one who will die" he yelled as he lunged at me. I sidestepped just in time causing him to ram headfirst into the arena wall. he turned around enraged and shot a dark pulse at me, I held up my paw and absorbed the attack. He stood there shocked, "h-how" he stuttered. He shook his head and active his blades. "I'll cut you to ribbons" he screamed as he charged at me, I dodged and extended my claws. He skidded on the floor then lunged for me again. I then ran towards him head on. It was time to finish this; I sidestepped and grabbed his arm. I twisted it causing a cracking sound. He fell to his knees and looked at me with fear in his eyes, but I would have no mercy on him. In a faction of a second my claw slit his throat, he fell to the ground dead. There was nothing else to do but open a portal and warp away.

Jake's POV

We found the lab just as the door was sealed. "Cass, little help" I asked. She smirked and stuck C4 to the door. It exploded like a pop can; we rushed inside ready for anything. Just as the smoke cleared I saw a door closing on the other side of the room. We stopped the door and perused the doctor, his black lab coat flowing behind him. He stopped in what looked like a control room and turned around. He had a wicked smile on his face as he spoke in a snide voice "you think you've really won anything" he taunted. We all looked at him curiously as he said "this is only one of many factories" He said proudly. He then pointed at me and said "you best watch you back because soon you'll be…" he was cut off as a bolt of compressed water blasted him through a window, I turned around Kelly had a smirk on her face. We heard him scream as he plummeted 20 feet down into the production line floor. We then heard a horrid cracking noise and a cry of agony. "Man he never shut up did he" Cassandra said. Just as we were about to look down to confirm his death an explosion shook the room. We heard an artificial voice say "reactor detonation t minus 4 minutes". We were just about to panic when a hole was blown open in the roof. Cold air rushed in as I looked up, a MRPA helicopter was above. It dropped and rope ladder and we all climbed up. Michael was sitting there when we reached the chopper "time to go" he yelled over the rotor. We strapped ourselves in just as the helicopter detached the ladder and flew away from the factory.

Gregavich's POV

Pain… pain was all I could feel as I laid there, I could not move at all. I knew this was it, death was about to take me. I was about to close my eyes when a Alakazam appeared above me. It said nothing as it grabbed my briefcase with the serums and then touched me. I passed out just as I felt my body go weightless.

Jake's POV

The factory erupted into a fireball throwing debris everywhere, the shockwave cause my ears to ache. Once I could hear again, I looked at my sister, she was smiling. Her blue eyes were filled with joy. "Let's go home" I said. She nodded at me as the pilot said "eta to base 2 hours"…..

? POV

I looked at the doctor in horror as he was laid on the operating table, this was not looking good. 3 broken ribs, left arm broken and his spine was in 4 pieces, he had minutes at best. He muttered something in a weak voice "bbb..briefcase….p- purple". I opened his briefcase and saw a vial with purple liquid. There was no time to think it over. I put it in a syringe and injected it into his right arm. He screamed in agony, second later a flash of light blinded me. When my sight returned to me a Mewtwo was laying on the table asleep but breathing. I was in shock, nothing could describe my reaction. Then the master appeared behind me and said "rest for now doctor,... you have a long recovery ahead".

 **author's note- wow three chapters in one upload, if that doesn't please you guys then i don't know what will. Im going to take a little** **break, so ill be back next week.**

 **leave a like comment or review. Im always pleased to know that some people like this story :)**


	17. Chapter 17

Chapter 17

 **Author's note- it's been 4 months since chapter 16**

Jake's POV

 _Just another day at the office_ I though as I snagged a shadow Breloom, "that's all of them" I said as the snag ball teleported away. This was the 3rd small outpost we had taken down in the last few months, and I have to say this is almost pointless. As long as we can't find the other factories cipher is still winning. Cassandra walked up to me as the soldiers swept through the site and said "I know how you feel, but we just have to take this day by day" she said in a hopeful voice. I sighed and said "I know" we loaded all the data from the outpost's computer and headed back to base.

Kelly's POV

I dodged the dragon pulse as I though _this is getting old_. Me and Lilly had been sparing for months and yet we still weren't allowed on missions. The director's explanation you ask, well he wants us to have total control over our new powers. I personally think he just is paranoid about two cipher experiments helping him. I shot an ice beam and it hit Lilly dead on she fell to the ground defeated. I quickly shifted back and gave her a heal potion. She shifted back and I helped her up as she said "you just always have the edge on me". I looked at her and said "you'll get better" she looked at me with determination in her eyes, but I could see the sadness she was clearly trying to hide. I can't even begin to understand her pain. Think about it kidnapped then tortured as a lab rat then when you finally escape you learn that you only family is dead, she has it worse than anyone. "Cipher will pay for everything they've done" I reassured her. She gave a weak smile then said "let go get some lunch". I nodded as we left the training room.

Victor's POV

I sat there at the foot of the table sizing up our situation. Even though the new factory was destroyed our production has not taken a major hit. As I sat there I heard a snide voice say "still twitching doctor" I looked over at Edward as he continued to taunt Gregavich "you know if you had just been half as smart as you claimed to be maybe you wouldn't have to be like this". The doctor banged his twitching hand on the table "w-w-what have you d-done to further the c-cause recently" he snapped back. Edward smirked and said "oh I don't know… not get my base blown up". The doctor was about to respond when Alice chimed in "you know doctor, you really should reconsider you position here". "You really don't deserve a spot at this table" she continued. I was about to speak when Gabriel chuckled and said "man for once I'm not the biggest freak here" he laughed hysterically at that statement. Just then the door behind me opened as we all stood up. The master walked in slowly with his four Bisharps around him, they took up positions in the corners of the room as the master walked to the head of the table. We were silent as his boots banged on the floor, his blue robes covering his arms. As he sat down he looked at Edward and spoke in a cold voice "Edward do you find such childish behavior necessary". Edward looked at the master and said "no, I just don't like failure" he said as he glared at the doctor. The master paused for a moment, the entire room was silent. "Edward what have you done to further our cause recently" he asked in an annoyed tone. Edward was scared for his life as his face was reflected in the master's dark glasses. The master averted his eyes to the doctor and said "his successes far outweigh his failure" no one said anything. "He completed the corruption engine design, doubled production of shadow Pokémon and most importantly, he perfected the phase 2 serums" he said. Edward was sweating as he asked him "what have you achieved in the last 7 months?" the master looked at me and said "Victor you are to continue the work on the snag machines" I nodded in response, as second in command I had the hardest job naturally. He then looked at Gregavich and said "doctor you are to train every day here at HQ to help your body adjust to your new powers". "y-yes m-m-master" he stuttered in response. He then gave out his last 3 orders, "Edward, Alice tour the other factory's and make sure production is at maximum". "Yes sir" they responded in unison. Then Gabriel spoke and asked "should I hunt for more shifters master?" the master nodded and was about to dismiss us when the doctor spoke up, "w-what ab-bout the f-four s-shifters" he asked. Edward chuckled and said "they are of no concern to us and…" the master raised his hand and said" quiet Edward, the doctor is right" Edward said nothing. The master then spoke to everyone saying "the biggest mistake of my life was failing to recognize a threat before it got out of hand". He looked at Gabriel again and said "Gabriel, find them and eliminate them". Gabriel laughed and said "with pleasure". The master then dismissed us. As he walked out he said "get to work"…..

 **im back but as soon as school starts updates will slow down, anyway leave a like and review it really makes me happy**


	18. Chapter 18

Chapter 18

Kelly's POV

 _Finally_ , I though as the chopper touched down. Me and Jake were on our first mission together in months, and I have to say I'm excited. Our job was to investigate another Cipher outpost, but this was different from the others. After Cass and her soldiers swept through they noticed a tunnel that went underground. They said that they needed us to reinforce them just in case. Cass was waiting for us when we arrived. She motioned us to follow as she said "we're detecting a dark matter signature down there, gear up we may have found another factory" I nodded as Jake tossed me some night vision goggles. Time to see what lurks below…

Jake's POV

As we entered the room I was speechless, there was nothing but servers and computers in the large office like room. As we fanned out I sat at the nearest computer and logged on. Not password protected at all, guess they though it was overkill. As I searched for useful information I found file after file about archeological digs and translated unknown runes. Most of them about a place called Turnback Cave what did this mean. After 10 minutes of downloads and scouring data I found what I have been searching months for, factory locations. There were 4 factories in total, one in Sinnoh, one in Jhoto, one in kanto, and one in Kalos. We grabbed the data and headed back up the elevator…..

Connor's POV

I breathed a sigh of relief as the soldiers left. Once they were gone I looked at what they took. Turnback Cave, dark matter, distortion world…. wait distortion world, then the truth dawned on me Cipher was stealing energy from me but I was only one option of getting dark matter. If Cipher continues what they're doing, there won't be any world for them to take over…

Kelly's POV

As we waited for the chopper to arrive I was on edge, Cipher has to know we found their data hub. I was about to relax when a black beam of energy shot out of the forest heading straight for Jake. I tackled him to the ground as the dark pulse shot over head. We stood up just as we saw a figure emerge from the woods. He had messy black hair that was not well kept; he was very skinny and had a wild look in his eyes. He was wearing a black leather jacket and denim pants that were raged and cut. He laughed manically at the top of his lungs as he looked at us. "Who are you" I demanded. He finally stopped laughing and spoke "my name is Gabriel and you two are not going anywhere"….


	19. Chapter 19

Chapter 19

Kelly's POV

The mere sight of the man in front of me put me on edge. His purple eyes made him even more unsettling. Cassandra was the first to speak and said "I know who you are". Gabriel chuckled and said "really, then you should show some respect to a Cipher prefect". We all took a step back as he laughed again. Gabriel smile and said "as I've said you three are not going anywhere, I've been assigned by the master to eliminate you so… that is what I must do". Me, Cass and Jake shifted almost on instinct ready to fight. Gabriel laughed hysterically as he said "well no more to say really." There was a flash of light and a Toxicroak was in his place. This was not going to be easy…..

Connor's POV

I looked at the three people from a distance cloaked by my illusion. This was going to be interesting to watch…

Jake's POV

Gabriel lunged at us in the blink of an eye, and had we not gone through extensive speed training he would have had the drop on us. We all dodged in various directions trying to out flank him. However he knew what we were planning and shot black smog out of his mouth creating a thick fog in an instant. I yelled out to the others "don't breath it in" as the smog obscured our view. My eyes were no good, so I closed my eyes and listened carefully. I was listening carefully for any disturbance around me, and then I heard a small shuffling behind me. It was moving fast circling me, and then it pounced. I slashed Gabriel with shadow claw knocking him on the ground. As he got to his feet a strong gust of wind dissipated the smog. Kelly in her shift form was smirking as the smog dissipated. Gabriel stood up and said "well I must say I'm impressed but it's time to stop messing around. We all tensed back as he said this, in an instant he appeared in front of me and kicked me launching me into the air. As I was flying he shot a focus blast at me, I could do nothing as the super-effective attack hid me in my side; I fell back down to earth defeated. As I laid there on the verge of blacking out I watched helplessly as my sister and Cassandra were knocked around by Gabriel. Kelly was knocked on her side and Cassandra was knocked unconscious by a focus blast. Mustering all my willpower I got to my feet shakily just as Gabriel began laughing again. He then ran towards Kelly with his arm barbs in front of him, I knew how potent toxicroak poison was. There was no time to think, I moved as fast as could. I moved in front of my sister just as I felt two sharp objects going into my side. The world started spinning and fell to the ground blacking out soon after.

Kelly's POV

I was in shock as I stood up. My brother was on the ground twitching as Gabriel pulled his barbs out of him. Something in me snapped, my mind was consumed by pure rage. I summoned as much power as I could, feeling the torrent of water within me. I let loose a feral roar, sending a hydro pump at Gabriel fully aware that this attack could kill him instantly. The bolt hit him dead center throwing him 20 feet and crashing through a tree there was a horrid cracking sound as Gabriel landed. He uttered a cry of agony as I ran towards him, fully committed to ending his life. As I came upon him he got to his feet, his left arm was twisted and limp. He looked at me with pure terror in his eyes. Before I could do anything he pressed a button on his arm band, there was a white flash and he was gone. As my mind came back to me I ran back to my brother shifting back in the process. As I reached him I saw Cassandra shift back and pull out a phone calling for a medivac. I looked at him and fear nearly overtook me, he was on the ground breathing heavily. I stood there over him as purple ooze came out of his wounds. My brother was dying and I couldn't even move or speak. We were running out of time…..

 **Authors note- another cliffhanger man I'm horrible….hahahahahahaahhahaha**

 **Anyway leave a review and share this story with anyone who you think may like it. I really appreciate all the views**


	20. Chapter 20

Chapter 20

Kelly's POV

I was still in shock as we arrived in the med bay. My brother still in his shift form, his chest barley rising and falling, as if breathing was all he had the strength to do. He was wheeled into the operating room and I was forced to watch helplessly behind a glass wall. The doctors were hurrying around the room, trying to extract the venom before it was too late. After 5 minutes I was told to leave as the surgery was starting…

2 hours later….

I was sitting outside the room awaiting the news. I heard shuffling inside, seconds later the doctor came out "he's alive but he doesn't have much time do you want to say goodbye" he asked solemnly. With tears in my eyes I said "no just leave him alone let him go in peace" the doctor nodded and yelled "clear the room". All the staff walked out and I was left alone in the waiting room contemplating when to go in.

Connor's POV

I warped into the operating room and looked at the dying shifter before me. He on death's door because he took his sister's place there and that is worth something. I grabbed a clean syringe and took some of my blood. I injected it in his chest; he flinched from the unexpected poke. "You've been given a second chance, use it wisely" I said quietly knowing full well he could not hear me. I then silently warped away leaving no trace behind….

Kelly's POV

I mustered the courage to go in 10 minutes later. I walked in the operating room planning to see my brother gone. However as I opened the door I heard coughing. I ran in and looked at my brother shocked and relived. He was lying on the table, his wounds stitched up and breathing calmly. I had nothing to say, the sight of him alive was too much and I snapped. I fell to my knees crying my eyes out, as the doctors returned. They dropped the body bag they were holding and finished stitching up the wounds. After almost 2 minutes I regained my composure and asked the doctor "what happened" he looked at me with a stunned expression "I honestly don't know but the venom is gone and his vitals are stabilized". I nodded and left the room happy as could be, my brother was alive and that was all that mattered.

Gabriel's POV

I was on my knees nursing my broken arm as the master stood above me. He was pacing as I gave my report. He finally spoke and said "you have failed severely Gabriel, I expect much better from you" I looked at him in fear as I said "but I poisoned one so I..." "Silence!" the master ordered. He then spoke with authority saying "you poisoned the least valuable target it is a near total failure" he barked at me. Before I could say anything else he delivered my punishment "you are to spend 2 months in solitary confinement with no treatment for your arm" he said coldly. He waved his hand and his guards dragged me away….


	21. Chapter 21

Chapter 21

Lilly's POV

As I walked into the director's office I was nervous. What could he possibly want from me? I opened the door gingerly fearing what the director had in store for me. As I entered his office he had a kind look on his face as if he was overjoyed to see me. He then said "please sit" as motioned to the chair in front of his desk. However his kind appearance was ruined by my abilities. Ever since the serum my psychic attributes were magnified greatly. I could read minds without even trying, not to mention my illusions. I could turn completely invisible and mimic the appearance of anyone I've seen before. As I sat down I could sense the negative emotions off the director. He was afraid…. but not of me. He seemed like he wanted me to do something very risky and was unsure if I was capable of it. He spoke to me with a calm but stern voice saying "Lilly I have a very important task for you". "What is it" I responded nervously. "I need you to go undercover in a cipher base and get all the information you can". I stood there dumbfounded not saying anything. He sighed almost as if he knew this would be my exact reaction. " I know it's a lot but you're the only one who can do this" he said in a dead serious tone. I finally managed to speak and said "I… I'll do it" he nodded and said "good, you leave in 3 days". He then spoke with authority saying "go and practice your illusions you're going to need them"…

Jake's POV

I sat there pounding on the punching bag releasing my rage on the bag of sand. Gabriel got away and I'm not allowed on missions for another week. Eventually a voice snapped me out of my thoughts. "Take a brake bro you're going to get bloody knuckles" I stopped my onslaught "should you be on a mission" I said casually. "Well after your big brother almost dies you tend to worry about him" she said in a half joking tone. I sighed and said "I told you I'm fine" I said in an annoyed tone. She looked at me with concern all over her face "that was enough venom to kill 3 people". She paused and said "I can tell something else is bothering you what is it?". "I just am mad I can't help you on missio…" she raised her hand and cut me off "no what is really bothering you" she demanded. I sighed and said "I just feel weird like something inside me is off…" she put her hand on my shoulder and said "you're still recovering just take it easy for once" I nodded slowly she was right. She then punched me on the shoulder and said "let's go out for some dinner leave the base for a change" I nodded and we walked out of the training room….

Victor's POV

I sauntered together the last wire and closed the access panel. With any luck this new snag machine would work. I went over to a table as a raichu was strapped down. I activated the snag machine, there was a flash and a pokeball sucked in the electric Pokémon. "Success" I said to my assistants. However my success was short lived, the pokeball exploded and a dead raichu was in its place. "Darn" I said banging on the table. I sighed as the dead Pokémon was carried away; this is just not my department. I then walked towards the doctor's room, as soon as Gregavich can keep his hands still I need his help.


	22. Chapter 22

Chapter 22

Lilly's POV

As we touched down near the factory I was shaking. What if I got caught? I quickly shook my head I could do this. Michael looked me in the eyes as he handed me my I.D card and said "you can do this just remember your training". I nodded and began to walk off as Michael gave me one last remainder "as soon as you get the data get out" he waved then boarded the chopper. I didn't bother to watch the chopper takeoff I had a job to do. I took a deep breath and shifted my appearance. In seconds I was a middle aged woman with blond hair and grey eyes, my name was Kathrine and I was a transfer from another base. After months of special training I had learned to keep my appearance shifted indefinitely. I also had to learn all the basic things about being a lab assistant which was not very hard. If seemed oblivious that was fine as I was supposed to be new. I had just been at the factory gate for less than a minute as the guards came out to greet me. I was sweating bullets but I used my illusions to cover it. "This is private property leave" one of them ordered I quickly responded with "alpha 4 zulu tango". Then then relaxed slightly and said "oh you're that new transfer ok sorry for the rough welcome" I breathed a sigh of relief and said "oh thank goodness I was worried you didn't get the message I was coming" they smiled and said "this way please" I walked through the gates and came to the door. The guards flashed their cards and went in. I walked towards the door and pulled out my I.D. _relax I told myself, they jumped the lady you pretending to be so the I.D is good_. I flashed my card and went in.

As soon as I reached the labs I was confronted by a man that looked nothing like a scientist he was broad shouldered, bald and was wearing a black suit with the cipher logo on it. "You are the new assistant I presume" I paused briefly and said "yes" he thought for a moment then said "excellent you will be assisting the head scientist in this facility". He then handed me a slip of paper and said "this is your room number, the doctor you will be serving under will arrive the day after tomorrow" I nodded and headed to my room this was going to be a while.

Edward's POV

As I walked out of the labs I was smiling production was at maximum and soon phase 3 would be underway. I was also pleased to meet a new trainee that was going to be Gregavich's assistant. She seemed to be capable from what I could tell. I hate Gregavich. He seems so careless about the plan he just wants to be a scientist, but I admit he is vital. Maybe his new powers will remind him how much he owes cipher. I then boarded my helicopter and took off heading for HQ. Things were going smoothly

Kelly's POV

At we sat down eating I could tell my brother was already feeling better. This was the best restaurant in Castilla city known especially for its ice cream. It was nice to just take a break and leave the base. We finished eating and left the restaurant. The base's location is secret so we when we want to go anywhere we have to go by chopper. We arrived in pinwheel forest with no trouble at all. I pulled out my phone and called for pickup. The chopper would arrive in 30 minutes. As we sat there in the soft grass with the stars above our heads we had a nice time of peace. This was a welcome break from our missions for sure. "You feeling better now" I asked my brother. He nodded but said nothing else. Soon enough the chopper arrived and it was time to go. Surprisingly enough Michael was there to pick us up. As we flew back he told us about Lilly's assignment saying we deserved to know. I just hope she can pull it off.

 **author's note- thanks for all the views leave a like or review it really makes my day to see some feedback**


	23. Chapter 23

Chapter 23

Lilly's POV

After breakfast I headed up to the labs I just hoped I wasn't with a scientist from that other factory man would that be awkward. I arrived in my designated room and waited for my new "boss" to arrive. I decided to get on a computer and see what I could access. As I was logging on I heard a voice behind me say "trying to get an early start I see" I shuddered at the sound of that voice. That vile snide voice that haunted my dreams, the one that tortured me for months like I was nothing more than a dumb animal this had to be a bad dream. I turned around hoping I was merely hearing things but he was there. Gergavich was there just smirking at me. It took every ounce of my training and restraint not to lunge at him and slaughter the monster in front of me. "Well, get a clipboard I need someone to take notes. I nodded and grabbed some notes. I have to keep calm, I have to keep calm I just kept saying that in my head. We went to the containment cells and I just followed not saying anything just taking notes. As I was around him I grew more and more concerned, how did he survive that fall? Kelly blasted him through a reinforced window and down into a cold metal floor. Worst of all I felt a massive amount of energy coming from him more than I've ever felt, but he's not a shifter. The serum, that's the only way he could be standing here. I just had to keep calm. Eventually he was done with me and said "I'm going to lunch I suggest you do the same" with that he turned and left. I have to get the data and leave NOW

Gregavich's POV

As I was eating I got a phone call from HQ. I went to my study and activated my video phone. "This is Gregavich" I said as the monitor came online. Soon the master appeared and said "doctor I have something important to tell you" I said nothing. "The mega stones are on their way along with your new bodyguard". I paused then said "bodyguard I am more than capable of defending myself". The master's face was emotionless as he said "I am well aware but this new bodyguard is experienced about mega evolution and Is unquestioningly loyal to me he will be seeing to base security". I simply nodded as he said "you are to continue your work on the synthetic mega stones and begin fabrication for the AD36115" with that the phone went dead. I just sighed, great another person who is just going to bother me, and try to tell me how to do my job.

Kelly's POV

As we stormed the outpost I was walking on air. Finally me Cass and Jake doing missions again just us doing our job. However as I snagged a shadow absol I heard a sound behind me. as I turned I felt a horrid pain in my shoulder. I fell to my knees as blood came out of my shoulder I was hit! The soldier was about to fire again when Jake tackled him to the ground. The soldier kicked Jake off and pulled out a stun baton ready to take him on. I then looked at my brother as he looked at me. Out of nowhere his eyes turned red and a black aura swirled around him. You could almost feel the pure rage from him as he lunged at the soldier tackling him to the ground. Without any hesitation he began to punch the soldier mercilessly beating him again and again. "Jake STOP" I yelled as he continued to attack the already unconscious soldier. He looked at me his eyes blood red and filled with hate, but as he saw me his eyes returned to normal and the aura dissipated. At that he passed out and collapsed. I stood up shakily the soldier was not breathing. Cassandra ran to me and said "I'll get a medivac ready for you". I shook my head and said "shifters heal fast I'll be fine enough to just fly back to base". She nodded than looked at Jake with fear in her eyes. What just happened to my brother?

 **authors note- thanks for all the views leave a like and review i love the feedack i will only be accepting 1 more OC as the new bodyguard is one so im going to be very picky**


	24. Chapter 24

Chapter 24

Gregavich's POV

I got a phone call after I woke up, he was nearly here. I just hoped this was someone who could follow my orders. I arrived at the helipad just as the chopper touched down. The door opened and my heart promptly sunk. A young man in black armor appeared his helmet concealing his face and a green espeon at his side. Of course the master sent his pet, just great. I walked up to him as my scientists took the mega stones from the helicopter, time to say hi. "Hello doctor it's been awhile" he said casually. "Indeed Ethan, now come with me" I said he nodded and followed me with his espeon in tow; this day was just getting better and better

Ethan's POV

As I followed the doctor to his office I was confused. Last time I met him I could sense his emotions and thoughts but now nothing he was blocking me form reading him somehow espeon couldn't get a read on him either, I shook my head it's nothing maybe he just is good at hiding his thoughts. As we entered his study he sat down at his desk and I remained standing. He sighed then said "so you're my new bodyguard, let's make some things clear right now." I stood there silent not knowing what to expect. "You are not to question me on any of my decisions not involving security, you are not to enter this study unless the door is open, and you follow my orders nobody else's except the master". I was scowling under my mask he was treating me like a pet. He then said "any questions no then get to the command center and stop wasting my time!" I nodded then turned and left too enraged to say anything.

As I entered the command center I went to my new desk and sat down with espeon at my feet. Then a soldier came up and said "sir this is your keycard" as he laid the laminated card on my desk he then turned and left. I then decided to go over the factory layout on my computer. Time to get up to speed with the factory specs…

Lilly's POV

As I was eating breakfast I could barely stop shaking. How was I going to keep my cool around the doctor I barely managed to stay cool yesterday and I've learned enough stress can break my illusion. I sighed and put up my tray. Time to play the odds…

Gregavich's POV

I left my study and went to the labs. Kathrine was there on time as usual, I handed her a pad and said "follow me we're going to the lower levels" she nodded and said "ok". We entered the elevator and descended to the labs. As we arrived the new test subjects were being strapped in to their chairs. I looked at Kathrine and handed her a vial. "Go, put this into the injector in holding cell 3" she nodded and went to the door as I went to the observation room. She put the serum in place then joined me. I pressed the remote and injected the serum into the girl. However the results were rather undesirable. The girl started glowing; a red light was emitted from her mouth and eyes as she screamed in pain. There was a horrid flash and an explosion. When the smoke cleared there was nothing but a black scorch mark on the floor. The room was silent, Kathrine was covering her mouth. I sighed and said "make a note of that, it seems the stronger legendary Pokémon DNA isn't compatible with my serum". I shook my head and said "back to the chemistry lab I suppose… Kathrine know this discovery requires experimentation" she nodded shakily in response. "Take the rest of the day off, you need it" she nodded and left the room. She looked like she needed to puke….

Lilly's POV

After my stomach was empty I retired to my room. I locked the door and dropped my illusion. I laid on my bed and wept for the rest of the day too shocked to do anything else…..


	25. Chapter 25

Chapter 25

Lilly's POV

I was taking notes when the doctor said "that's all for today, take this data pad to a computer and upload it to the server" he then handed me the data pad and a silver keycard and said "this is a server access card please return it to my office once you are done" with that he turned and left. I casually walked towards the computer room trying to not attract attention this was my chance….

Ethan's POV

I just had doing my rounds when I entered the command center and was called over to a tech specialist's desk. "What is it?" I said to him. he pointed to his screen and said "there was just a massive data copy in the server room" "WHAT who" I demanded. He shook his head and said "I can't tell we just have 10 server access cards that are given out as needed". She then said "after the data withdraw I intercepted this…." he hit play and a scrambled voice said "this is MRPA agent 21 I have the data and I heading to extraction point bravo….." she then picked up a phone and said "ill alert the doctor…" "NO" I ordered. She put the phone down "why we need administrator access to initiate lockdown?" I then responded "the doctor is a selfish egomaniac ill see to this myself then prove to him how wrong he was to boss me around" I then yelled "station guards at every exit… you four with me" 4 soldiers followed me as we ran towards the server room. This spy is going nowhere….

Lilly's POV

I left the transmitter in the server room to buy me some time I then went to the nearest exit. As I neared the exit two guards stopped me "sorry but this area is on lock down" I sighed and said "ok then" in a blink of an eye I threw them against the wall with my telekinesis knocking them out cold. I was about to open the door when I heard a voice say "that's far enough" I turned and saw a man cloaked in black armor but he was much shorter and wearing a different armor than the man that abducted me. He then drew a sword and said "you are not going anywhere" I was about to raise my hands when one of his soldiers knocked him out with a punch to the back of his neck. I stood there in shock as the cipher soldier knocked out the other 3 soldiers with a blast of black energy. "Who are you" I said there was a flash and a Zoroark was standing before me. I was speechless as he said "I must say you blended in well for a Latias" "t-thanks" I stuttered. We heard someone yell "this way" he then calmly said "well time to go" he waved his paw and a portal materialized in front of us. He then motioned for me to follow I said nothing but nodded. We went through the portal then arrived in the forest outside the factory. The dark portal closed the second we went through it "Thanks" I said he smiled and said "the extraction point is 13 miles that way you can fly the rest right" I nodded and shifted into a latias he then said" stay low so they can't track you" with that he teleported away. I took to the sky skimming above the trees. I made it out and that was all that mattered…..

Jake's POV

I was in the med bay for another checkup. I sighed as the doctor took yet another blood sample. "How many golbats you feeding doc" I said jokingly he put a bandage on and took the blood away without saying a word. Now alone I sat there thinking _what's happening to me why did I lose it like that._ I was snapped from my thoughts by Michael entering and saying "you are one sick puppy" his voice rich with sarcasm. "Nice to see you too" I said sadly. He walked up and punched me in the shoulder and said "keep your chin up the doc will figure this out" I gave a light smile and said "yea I hope so, I hope so"

Gregavich's POV

Ethan woke up as soon as the master arrived. I had never seen the master this enraged. Ethan was on his knees begging with his helmet off. Fear in his eyes and his mutant ears drooping like a scared cat as the master paced in front of him, the banging of his boots was the only sound in the room. "Sir why is this my fault, he was the one who didn't notice the infiltrator" he said pointing at me as whined like a wounded dog. "He should be…" "LOWER YOUR TONE BOY" the master ordered. Ethan stood up and defiantly said "this is his fault not mine you are wrong". I stepped back a few feet as he said that even the master's bisharps were standing back afraid of his reaction to Ethan's rebuttal. The master then took his black glasses off revealing his icy blue eyes. "Choose you next words very carefully brat" Ethan once again stated "you are wron…" the master raised his hand hurling Ethan into the air slamming him against the celling, then with a flick of his wrist Ethan's arm was twisted into a grotesque shape then changed back. Ethan landed hard shading tears and wailing in pain. The master put his glasses back on and said "how does it feel to have your arm broken then fused back together" Ethan said nothing as he continued to cry in agony. The master then turned to me and said "doctor load up all valuables in the trucks then scuttle the factory. I nodded but said nothing, he then turned to his bisharps and said "take him to my chopper he will be spending time in the brig"….

 **Author's notes- man that was brutal even for Ardos**

 **Sorry about the delay life has just been getting in the way of my writing, thanks for all the views leave some reviews I love the feedback** **I made this chapter extra-long for you guys so I would love if we could reach 1000 views.**


	26. Chapter 26

Chapter 26

Lilly's POV

As I handed the flash drive to the director he was ecstatic. "Well done Lily, I knew you could do it" I paused did I really deserve the praise after what I did. Malcom seemed to notice and asked "what's wrong you accomplished your mission should be happy" I was on the verge of tears as I said "at what cost, I had to murder someone to get it". Malcom sighed and responded "it wasn't you fault you did what had to be done, it was just another cipher soldier" he reassured me. "NO IT WAS NOT" I screamed with tears in my eyes. Malcom said nothing. "It was a girl younger than me, I had to prep the injector for the serum that killed her" I said as I wept. Malcom paused then spoke with authority "you had to do horrible thing I understand that". I looked at him right in the eyes as he continued "we are in a time of difficult choices, sometimes impossible ones". He then stood up and said "we have to live with those choices, but if we give up now that poor girl died for nothing" I nodded slowly he was right. As he left his office he said "take some time to yourself but I need you back soon" with that he shut the door leaving me alone…

Michael's POV

As we went over the data in the command center the room was silent. Lilly had scored the jackpot, both of the remaining factories' defenses and layouts were now revealed. Malcom was briefing us on the missions factory by factory. After he was done with the factories he said "unfortunately Lilly did not ascertain the location of cipher's primary base". I sighed as Malcom continued "we need to move quickly before cipher scuttles their factories they already destroyed the factory Lilly was at. He then gave us our assignments "Michael you and Cassandra are taking the factory in Kanto" I nodded in response as he turned to Jake and Kelly. "You two are heading to Jhoto" they quickly responded with "yes sir". Malcom then stood up and said "wheels up at 0-8 hundred hours. With that everyone left the command center. It's time to break cipher's backbone…..

Ethan's POV

As I sat in the cold stone cell, I was mulling over the choices I've made. I've got to say I made a lot of bad ones. First was thinking my father was really doing the right thing. After all the pain he gave me, I had no regrets killing him. After that I had a chance to start fresh, but I wasted it. I got in trouble with the law and I went to prison on a life sentence. Then cipher found me. Gregavich's bodyguard busted me out. I may have gotten on the master's good side but me and Gregavich never got along. He was the one who oversaw my extra training; let's just say I was not a willing student. I then heard a voice say "so finally got on his bad side huh". I sighed and said "shut up lance". He stood up and looked at me from another cell. He looked rough; his old uniform was dirty and ragged and I could almost see his ribs. He smiled and said "he tossed you aside just like he tossed me aside and now you'll rot here just like I have". I was about to snap back when Gabriel walked in. He looked at me with an evil smirk then turned to Lance. He opened his cell and said "your sentence is up you may serve master Ardos again". Lance spat on him and said "over my dead body" Gabriel laughed hysterically then said "ok then…". In the blink of an eye he shifted into a toxicroak and stabbed Lance with his barbs. Lance fell to the ground as the poison oozed out of his wounds. He fell on the floor his eyes turned purple and he stopped moving. Gabriel shifted back into a human and left laughing at the top of his lungs. Lance was gone and I was all alone.

 **Author's notes**

 **I have to say sorry for the long wait. School has been tough the last few months. I will try my best to update more frequently.**

 **Happy holidays everybody!**


	27. Author's Note and Announcement

Author's note and Announcement

To all my fans a sincere thank you for your support over the course of this story. It's incredible that we"ve breached 1000 views in just a few months. You guys are amazing!

Now for the bad news, i'm afraid that i've hit a roadblock with the story and it has reached its end. However this is not the end for pokeshifters, far from it. Book 2 will come eventually but i cannot confirm a time frame. It will come eventually. I would guess around 3-9 months at least.

In other news i am considering 2 projects in the very near future. One being another pokemon fic, and the other being a fanfic of my second favorite franchise RWBY.

I need YOUR help to decide, PM me what you would like to see and i will decide. The first fic to get 8 PM recommendations will be chosen.

Thanks


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